Merlin Holmes: The Secret
by There-is-magic-in-your-smile
Summary: This is a sequel to Merlin Holmes: The Other One. The brothers reunited but one thing keeps racing through Merlin's mind: do they know?
1. Chapter 1

Merlin Holmes: The Secret

Chapter One: The Other One

_"He's our brother." Mycroft said bluntly. _

The words rung sliently around John's head while the Holmes brothers looked at John, waiting to see how he would react, however John stayed silent looking blankly forward not even blinking. _Brother... How could I not see this?_ John thought. Merlin looks a lot like Sherlock, John had even thought so when they first met. _The way Sherlock reacted should have made it a bit more obvious. I even noticed it. _John thought back to how Sherlock reacted to seeing Merlin, Sherlock had gone into shock and stared at Merlin for a few minutes. John turned his gazed towards Merlin. Merlin looked as stunned as John felt staring at Mycroft, his blue eyes wide and his face had gone paler then what it was originally. _Anyone could mistaken him for a corpse if he wasn't breathing. _ John's thoughts continued to race through his mind as he thought about Sherlock and Mycroft, who were talking as though John and Merlin wasn't in the room. _It seems that Merlin didn't know. Poor kid._

"John." Sherlock snapped John from his thoughts. John looked up to see Sherlock staring at him with a puzzled look.

"Yes?" John asked, not quite understanding why Sherlock and Mycroft were staring at him as if he had said something strange.

"Did you hear what I said?" Mycroft asked, sounding slightly annoyed as if John was a small child throwing a tantrum. _What did he say? Urgh. Great now he's gonna think I'm more of an idiot then what he already does. _

John sighed and shook his head. Mycroft looked a bit more annoyed now, thinking that John didn't pay attention because he didn't care. John did care but he was more confused by the matter in which he found himself and by the looks of it so was Merlin.

"Uh. What did you say?" Merlin hesintly asked. Merlin didn't quite know what to make of the strange situation he found himself in, but something else was bothering him more - did they know?


	2. Chapter 2

**Author's Note: Hiya! I'm sorry that this is a bit of a long chapter! Also I'm not too confident about this chapter so I would really appreciate it if you could tell me what you think! Enjoy!**

Chapter Two: The Beginning of the Puzzle

John watched Merlin for a bit. Merlin stared at Mycroft waiting for him to answer. Now John thought about it Merlin looked a lot like Sherlock, more than he had realised. Merlin has the same face shape with quite prominent cheekbones, he has the same black hair and they have similar eyes. However Merlin's hair is straight and his eyes are larger and rounder. Also Merlin's ears stick out more than Sherlock's. John was suddenly aware that someone was staring at him, he could feel their gaze on him. John took his attention away from Merlin and diverted his gaze to Mycroft, who was looking at with an eyebrow raised. _Here we go. _John braced himself for whatever Mycroft had to say.

"Do you ever listen Doctor Watson?" Mycroft said with a sigh. John knew that when Mycroft called him 'Doctor Watson' it was because he was annoyed or lacking in paitence.

"Yes. However that would depend on if your being a pompus idiot." John replied. This got a smile out of Sherlock and Merlin. Sherlock often enjoyed the banter between John and Mycroft, he even likes having a bit of banter with his older brother.

"Moving on. We need to decide on what to do with Merlin." Mycroft said with a roll of his eyes.

"Do I get a say? You do know I'm in the room right?" Merlin asked a little sarcastically. _Good point. _John thought to Merlin. Mycroft had been talking like Merlin wasn't there, almost as if he were an inaminate object he was trying to clean his hands of.

"Of course you do. It's your life." John replied. Mycroft looked at John as if he said something idiotic. _Don't give me that look again._ John, who was starting to get frustrated with him, thought at Mycroft. Mycroft often looked down at people, including John, because he had 'a minor position in the government' - so he basically ran the entire country.

"Yes, I suppose it is your life." Mycroft said still looking at John. "So, what do you want to do?"

"You know it's rude not looking at the person your talking to right?" John asked Mycroft, who was still looking at him. _It's slightly disturbing. _John stared back at the oldest Holmes brother. _Do you not blink or something? _John noticed. Mycroft rolled his eyes and sighed under his breath.

"Uh, I think I'd like to leave this room at this moment in time." Merlin said watching John and Mycroft. John knew Mycroft wouldn't let Merlin just continue doing what he was already doing. Merlin looked very uncomfortable sat in the armchair that was slightly too big for him. John didn't blame him Mycroft made many people uncomfortable, including John when they had first met (not that Mycroft knew obviously, John would never hear the end of it).

"Mycroft won't let you leave jus like that." Sherlock said to Merlin. "Also I would like to ask you some questions, if that's ok with you?"

"I suppose so." Merlin said after a moments thought. Sherlock sat down in the chair opposite Merlin and studied him for a few minutes. Merlin seemed to become more uncomfortable each minute that Sherlock stared at him in silence.

"What did you know about your family before today?" Sherlock finally asked.

"I was told they died a couple weeks after I was born." Merlin replied.

"Well that's wrong, their very much alive." Mycroft interrupted.

"Yes." Sherlock said with a glance at Mycroft as if to say shut up.

"Well that's what it said on the note that was pinned to me." Merlin said staring back at Sherlock. Sherlock raised an eyebrow at this and lent forward with his hands infront of face, one of his favourite positions when he was thinking.

"I suppose they would do that." Sherlock said thoughtfully. Merlin gave him a puzzled look. "It's what happens on their boring tv shows." Sherlock said to explain.

"Oh. I've never seen one." Merin said.

"How did you end up on the streets?" Sherlock asked, completely ignoring Merlin.

"Oh. I ran away from the orphanage."

"Why?" Sherlock pressed.

"It was horrible there. I never had much food, I got punched and kicked by the other kids as well as other things." Merlin said. His eyes flashed in pain of the memories, but the pain soon left his eyes again.

"Were you in Ireland?" Sherlock asked. _What? Ireland? Where did you get that from?_ John thought. "He still has a faint irish accent." Sherlock said as if he read John's mind.

"Yeah I was. I left Ireland when I was about sixteen or seventeen." Merlin replied. John noticed his irish accent now Sherlock mentioned it. Sherlock sat in silence for five minutes, thinking about everything Merlin had told him. Sherlock sorted out what was probably going to be important later and stored it in his mind palace then he deleted everything that he didn't need. Sherlock thought about his parents and how they had managed to keep this from for as long as they had done. When Sherlock was about twenty he found out he had another brother. He had found a document concerning a pregnancy and when he had shown it to his mother she told him what he wanted to know, except where his brother was. It bothered Sherlock that his parents had managed to keep this from him for as long as they did, however Sherlock soon forgot about it when he started helping the police. He never completely forgot though, he had always remembered that he had a another brother somewhere.

"How did you get to England?" Mycroft asked, probably to find out if there was a security threat or not.

"I snuck onto a trading boat, potato traders if I remember correctly." Merlin replied.

Sherlock still had question for Merlin but he wanted to put some of the pieces together so he could get to the question he really wanted an answer to - what was the 'special skill' that his mother had told him about?


	3. Chapter 3

**Author's Note: Sorry this is such a short chapter but it came to a natural end. I'm writing chapter four at the moment so you'll get it soon!  
**

Chapter Three: A New Piece of the Puzzle

John had many questions for Merlin, particularly about his injuries and how he's able to survive on barely any food, but decided to keep them to himself for now. He watched as Mycroft interogated Merlin about the boat he had snuck onto and no matter how many times Merlin told him that he couldn't remember much Mycroft kept going. John could see that Merlin really wanted to leave and pretend this day hadn't happened. _It's happened and I'm sorry but you have to put up with it. _John thought to Merlin, he felt sorry for Merlin because he woke up believing that he had no family in the world to find out he has one of the strangest families in the world. Also John could tell Merlin felt overwhelmed and was quite confused but Mycroft and Sherlock just wanted their answers.

"Would you like some water Merlin?" John asked to get Mycroft to be silent for a moment, not matter how short lived it would be.

"Um... Yes please Mr. Watson" Merlin replied. _Mr. Watson sounds wrong, I haven't been called that for a long time. _

"You can call me John. Mr. Watson sounds like a grumpy teacher." John said to Merlin. Merlin gave John a small smile in reply as John fetched him a glass of water. John had taken to Merlin, he wasn't like his brothers for one he hade manners and he knew how to smile, almost. John handed Merlin the glass and Mycroft raised his eyebrow at John in an annoyed fashion.

"Are you quite done?" Mycroft asked.

"Yeah, I thought I'd try to shut you up for a bit." John said. "Oh well, the silence was short but sweet." Mycroft rolled his eyes at John while Merlin tried to hold his laughter back. _That's the first you've smiled properly for a good five or ten minutes._ John thought at Merlin.

"So are you." Sherlock said to Mycroft in a matter of fact sort of way. Clearly Sherlock had more important questions than any security threats.

"My- our mother told me you have a 'special gift' when I first discovered you exist." Sherlock said to Merlin, whose eyes had doubled in size and looked very worried. "I would ask if you know what I'm talking about but judging by your reaction I think it's fairly obvious that you do." Sherlock continued. Merlin cheeks turned slightly pink when he realised that he was staring at Sherlock.

"Sherlock what are you talking about?" Mycroft asked his younger brother. Sherlock raised an eyebrow at him, clearly Sherlock thought Mycroft knew about this apparently he was wrong.

"Don't you know? I thought you would have known." Sherlock said in a patronising tone. Mycroft rolled his eyes. "Merlin, what is this 'special gift' that my- I mean our mother told me about?"

"Hang on. You don't know what it is either?" John asked Sherlock astounded that he didn't know. _This is a rare occasion._ John thought.

"Would it be easier if I showed you?" Merlin asked. Merlin had a reluctant look on his face as he really didn't want to have to do this but there was no hope in hell that they would believe him if he just told them. _What on earth is this 'special gift' Sherlock keeps talking about?_

"You could just tell us." Mycroft said to Merlin sounding slightly frustrated with the whole situation.

"You wouldn't believe me if I did." Merlin said.

This caught everyone's attention.


	4. Chapter 4

**Author's Note: Hello! Sorry that this has taken so long but I had loads of other stuff to be worried about so this took a backseat for a bit. But I've done it now so enjoy!  
**

Chapter Four: The Discovery

John watched Sherlock consider the options: force Merlin to tell them or let him show them. Clearly Sherlock didn't like either of these options, but eventually Sherlock said: "Show us then."  
Merlin sighed in relief and motioned for John and Mycroft to come closer. John positioned himself on Merlin's left side and Mycroft stood on his right.

"You have to promise not to freak out or anything." Merlin said to John.

"Oh right. I... um promise not to freak out." John replied. Merlin had started to make John feel nervous. Merlin nodded satisfied with John's promise.  
Merlin focused on his clenched hand that he held out in front of himself. Sherlock watched Merlin carefully as he wispered something. Sherlock saw Merlin's eyes glow a gold - amber colour, the coloured danced in his eyes and quickly faded away again. When Merlin opened his hand there was a small flame, flickering from his breaths. The room went still and silent, everyone was looking at the impossible little flame that was dancing in Merlin's palm. Sherlock's eyes had almost doubled in size taking in all the information that he was seeing, storing it in his mind palace for later. Mycroft watched the flame thinking about how his parents had managed to keep this for all these years, even Sherlock knew about the gift, even if he didn't know what it was he still knew about it before Mycroft. _But I'm the smart one!_ Mycroft thought to himself outstanded by everything that had happened in a few short minutes. _How? I don't understand... this doesn't make any sense..._ John's thoughts raced through his mind as he watched the little flame. John thought about everything he knew about tricks that street performers do and professional magicians but he'd never seen anyone produce a flame like that. _What's going on? What's Sherlock planning?_ John thought and looked up to see that the consultant dectective looking as stunned as he felt. John had never seen his best friend seem so shocked before, nothing really phased Sherlock - _You kept a decapitated head in the fridge and this is what shocks you?_ John thought.

Merlin closed his palm after what felt like hours to John but had only been a few minutes in reality. Merlin looked at each person in turn to see their reactions. Sherlock was still staring at the space where Merlin's hand had been his eyes still wide with shock. Mycroft had started to walk away from Merlin and sat down at his desk again, his head resting on his hands. John turned his head towards Merlin and looked at him, speechless. Merlin gave him a sheepish smile, he had nothing to say, he didn't know what they wanted him to say. Merlin didn't know how to explain how he can do it, it was a long story one which he didn't want to tell.

"Right..." John sighed with a small shake of his head. John started to walk away back to the chair he had been sat in. He watched Merlin carefully, not really knowing what to make of him, while Merlin watched him just as carefully. _Poor kid._ John thought, thinking about Merlin's life. John had many questions about what Merlin could and could not do but his main concern was: was Merlin safe? John thought about asking him when Mycroft stopped him.

"I assume that you are in control of this... talent." Mycroft said in his usual monotone voice.

"Mostly." Merlin replied looking up at Mycroft. Mycroft replied with a raised eyebrow. "Well... once when I was ill I had no control over it, but I seem to be able to control now."

"So there could be a situation where you can't control it?" John asked with a concerned tone.

"Uh... yes?" Merlin replied clearly unsure of the right answer.

John raised his eyebrow and looked at Sherlock, who hadn't spoken for a while now. Sherlock was looking towards Merlin thinking about what he had seen. It didn't make sense to him how a flame can just appear in a man's hand. John was still watching him when he shot up and grabbed Merlin's hand.

"There's no burn. How can there be no burn?" Sherlock said staring at Merlin's palm. Merlin looked shocked and tried to pull his hand away but Sherlock held onto it.

"I don't know! There never is!" Merlin said in a state of panic. Sherlock examined his hand for a moment longer then let go and stood up straight.

"So.. now what?" John asked, looking at Mycroft then at Sherlock.

"Well that depends on Merlin's ability to control his talent." Mycroft said.

"What do you mean? What's that got to do with anything?" Merlin replied in a almost panicked tone of voice.

"Are you a danger to anyone, the country or yourself?" Mycroft asked staring at Merlin, trying to be intimidating. John had to hold back his laughter, he found Mycroft trying to intimidate people hilarious because he looked strange while trying.

"No! Of course not!" Merlin replied sounding insulted by the mere suggestion of it. John couldn't see Merlin hurting anyone he seemed to kind to do such a thing.

"Well then you're free to go." Mycroft said.

"You haven't arrested him Mycroft." John pointed out to him. Mycroft sighed and rolled his eyes.

"Well then Merlin, what do _you_ want to do?" Sherlock asked.


	5. Chapter 5

**Author's Note: Hello! I'm soo sorry this took so long! I've had exams and loads of stuff started happening all at once! But hopefully this chapter makes up for it! Enjoy!**

Chapter Five: John

Merlin sat looking at Sherlock, not blinking just looking at him as if he wasn't really there. Merlin looked as though he had been asked the most important question in the whole entire universe. John watched him carefully, concerned about what he was going to do. He didn't really want Merlin just to return to his life on the streets. Merlin lent back into the chair and started to think. He could use this opportunity to get off the streets, but he didn't want to owe Sherlock or Mycroft anything. On the other hand he knew that Mycroft was going to keep an eye on him now, which was something Merlin didn't really like the sound of.

"I... erm... I think I'll just..." Merlin stammered looking helplessly at John. John could see that Merlin was overwhelmed and had know idea what to do next. Before Merlin could say anything else John said:

"I think you should stay a Baker Street for a while. I'm quite concerned about the cuts and bruises you have, particularly the one on your side. Also your extremely underweight so I would like to keep an eye on you." John looked at Sherlock who had raised his eyebrow at him, clearly wanting to know why John had stepped in. _You'll figure it out. Anyway you probably want to learn more about Merlin. _John thought at Sherlock who had now turned his attention back to Merlin.

"Well... I think... it's just tha-" Merlin had started to stammer out a reply when Sherlock interrupted him.

"That's settled then you'll stay at Baker Street. Come on." Sherlock said as he stood up and strolled across the room. John was almost certain that this wasn't actually what Merlin wanted to do but it will do for the time being. Merlin said goodbye to Mycroft and followed John out of the room. Sherlock waved a taxi down and they set off for Baker Street. Merlin looked relieved to be out of the Diogenes Club and away from Mycroft, however he was still being studied by Sherlock and his stare made Merlin feel very uncomfortable and he started to fidget. Merlin looked out of the window watching London speed past him. All the different colours of the shops and all the different lights blended together as the taxi sped along the road. Soon they arrived at Baker Street, Mrs Hudson came into the hallway when she heard the door open and looked shocked to see Merlin again. She had some flour on her purple cardigan and was holding a rolling pin. John assumed she was making more bread, he was more than sure that they had enough bread to last them the month with the amount that Mrs. Hudson liked to make.

"Oh! Hello dear, I didn't expect to see you so soon." Mrs. Hudson said looking at Merlin.

"He's going to be staying here for a while so that John can keep an eye on him." Sherlock said bluntly as walked up the stairs, not looking at Mrs. Hudson once.

"If that's ok with you ma'am?" Merlin asked Mrs. Hudson, who seemed more than happy to have Merlin around.

"Of course, you stay as long as you need to." Mrs. Hudson replied with a smile.

John took Merlin upstairs to the living room and Merlin sat down on the sofa where he had been sat the first time he was there. John left the room to get Merlin a blanket and pillow for the night, leaving him with Sherlock. Merlin gazed out of the window watching some birds flying around when he felt a pair of eyes on him. He turned around to see Sherlock watching him with an intense stare. It started to make Merlin uncomfortable and he started to fidget again. Merlin could tell that Sherlock was studying him, trying to figure him out, and he started to wish John hadn't left. Merlin turned away from Sherlock once more to watch the birds. Sherlock never took his eyes off Merlin while John was out of the room, he couldn't understand what Merlin was or what his 'skill' was and it had began to annoy him. John walked into the room with his arms full with a blanket and pillow which made it hard for John to see where he was going. However he still noticed Sherlock staring at Merlin, he put the blanket and pillow down on the sofa next to Merlin and gave Sherlock a stern look. Sherlock quickly turned around and got back to his experiment from earlier in the day.

"Thank you." Merlin said, smiling up at John.

"Your welcome." John replied. "Don't mind him, he's always like this." John whispered and gestured towards Sherlock. This was more or less the truth, whenever they met someone new Sherlock liked to figure them out which usually took a matter of seconds or a couple of minutes. Most people Sherlock figured out within moments, like John, but one or two people he couldn't figure out so easily, like the Woman and now apparently Merlin.

John walked over to his chair, sat down and picked up the newspaper. On the front page there was a report on the latest case solved by Detective Inspector Lestrade. This was one of the few that Lestrade didn't need Sherlock's help. The detective liked to make out that Lestrade needed help on all of his cases which Sherlock exaggerated quite a lot of the time, saying things like 'he wouldn't have been able to solve that without my help' or 'they hadn't even found any useful evidence' to John after they had helped with a case. When John had first started helping Sherlock he would exaggerate it more to impress him, but he had done it less often and calmed the exaggerations down now. John was happy to have no cases for a couple of days, Sherlock on the other hand hated it. It usually drove him mad after a day. Hence the bullet holes in the wall and the experiments in the kitchen, the longer they went without a case the more bizarre the experiments became. John had stopped asking about the experiments, unless they were to do with a case, because the answer was usually quite strange and disturbing. Merlin continued to stare out of the window not really sure what to do with himself. He wasn't used to this. He hadn't stayed in a flat before and had been on the streets for so long all he had ever done during the day was find food, avoided police and made sure he had a safe(ish) place to sleep. John looked at Merlin from behind his newspaper. Merlin had dirt on his face and his hair suck out everywhere. He hadn't had a wash for a long time and with all the cuts he had this was a problem.

John left the room again to get the shower ready for Merlin. John had started to wonder about his life on the streets again, how often did he wash? Merlin really wished John would just stay in the room, he wasn't sure he liked being left alone with Sherlock. The silence between the two men was awkward verging on unbearable.

"So. What is it?" Said Sherlock breaking the silence very suddenly.

"Uh. Excuse me?" Merlin replied not understanding what Sherlock was referring to.

"This _skill_ of yours. What is it?" Sherlock said.

"You mean my magic?"

"There's no such thing." Sherlock replied ubrutly.

"But I showed you it. How can you deny the evidence of your eyes?" Merlin said, seeming slightly shocked that Sherlock didn't believe him.  
This was also bothering Sherlock. On one hand he could always trust his senses and what he saw. On the other hand what Merlin had done was impossible and Sherlock couldn't believe what his eyes told him. Could he trust anything his senses told him about his younger brother? John and Mycroft had seen the flame too, could they trust their senses? John had seemed to believe Merlin. _John would believe anything. Particularly something like this. _Sherlock thought to himself. Sherlock was too busy thinking over the days events to notice that John had come back into the room or that Merlin had walked out moments afterwards.

When Merlin opened the door white steam came floating towards him. John had already turned on the shower and set out everything Merlin would need. John had told Merlin to leave his clothes by the door so that John could get them and wash them, however he didn't feel comfortable doing this and decided he would keep them close to him. Merlin slid the little bolt across and started to undress. He noticed that there was a small patch of blood on the back of his shirt once he had pulled it over his head, wincing with the pain of his newest bruise. He turned to look at his back in the mirror, one of the many cuts on his back had started to bleed. _It's only small... It'll be fine _Merlin reassured himself not wanting to worry John. He got into the shower the hot water running down his pale form. The water had a pink tinge to it from the blood as Merlin let the water clean his cut. Merlin rubbed the fruit scented shampoo into dark hair and watched the bubbles slide down his bruised chest. He could see the bruise forming on his side now along side the others and all of the cuts. As the water washed away his blood and the bubbles from his hair Merlin started to think about the days events. _I have two brothers... why did no one tell me?_ He started the day with no family and he now has two brothers, it was a lot to take in. _They knew about me. Why didn't they look for me? _Merlin thought starting to get angry. _All those years on the streets... alone. They never came looking for me._ He felt rage surging through him. John tried to open the door and snapped Merlin out of his thoughts.  
"Merlin? Everything okay?" John's muffled voice came through the door.

"Yeah. Everythings fine." Merlin heard John walk away. He quickly washed his body and got out and dried himself. Wincing as he put his clothes back on Merlin hurried out of the bathroom back into the lounge, where he was greeted with the smell of something toasted.

"Grilled cheese sandwhich." John nodded towards a plate.

"Thanks." Merlin replied. He sat down on the sofa once more and ate in silence. A little while later John left to go to bed and Mrs. Hudson came up to make Sherlock go to sleep. Merlin was happy to be alone again so he could get used to his surroundings. He laid down under the blanket and allowed himself to drift into a deep sleep for the first time in a long time.

"Morning." Merlin said when John walked in.

"Good morning Merlin." John replied sleepily. He walked over to the kitchen and put some toast on, he only did two slices it was unlikely that Sherlock would be eating breakfast.  
"Let me look at your side." John said turning to Merlin.

"Why? I thought you said it was fine." Merlin replied with a worried expression.

"It is but I want to make sure it doesn't start swelling." John replied as he walked over to Merlin. Reluctantly Merlin pulled his shirt over his head and left it hanging off the end of his arms. John knelt down in front of him and gently pressed his side. It was still sore and the bruise was very obvious and quite big now, however there was no sign of swelling.  
"It's all good." John said and walked around to the back of the sofa to retrieve his laptop. As he stood up with his laptop in his hands he noticed a bright red cut on Merlin's back.  
"Why didn't you tell me that your back has been bleeding?" John asked Merlin feeling slightly annoyed that he didn't think to tell him.

"Because it's not important," Merlin said, "And you've been so nice to me I didn't want to worry you." Merlin added quickly noticing John's expression.

"It is important, it could get infected." John said, still slightly annoyed. However their conversation was cut short by John's mobile phone going off.  
"Yes?" John said into the device. "Oh hello Harry." He added after a moment of silence.  
"Yeah of course." John hung up the phone. "That was my sister, she wants me to meet her at a cafe down the road." John told Merlin seeing his curious expression.  
"Look if Sherlock asks I'm with my sister." John said as he headed out the door.

About an hour later Sherlock came into the lounge and went straight to his experiments. Merlin noticed that Sherlock seemed to talk to himself quite a lot and found himself smiling at the strange one sided converstaion the detective was having. Merlin spent a lot of the day downstairs with Mrs. Hudson helping in anyway he could to say thanks for letting him stay, also he wanted to avoid Sherlock staring at him.

John started to head back to the flat when someone called his name.  
"John. John Watson?" It sounded vaguely familiar. It had a playful tone and a hint of an accent that John couldn't recognise. Even though he knew it was probably a bad idea John slowly headed towards the voice. _I'm probably going to regret this.._ John thought as he headed towards the voice. There was a large black car parked alongside the pavement, like the ones Mycroft uses. _Mycroft? Really, what now? _When John got to the car however one of Mycroft's people wasn't there to greet him.

"Hello John." The voice said. "Did you miss me?"


End file.
